Gupta A, Gupta V, Pa SK, Narayan J, Potukuchi SM, Verma V., In-Silico structure
prediction of p27SJ, a novel protein in St Johnís Wort that suppresses
expression of HIV-1 genome, Onl J Bioinform.,
19(3):281-288,
2018. Hypericumperforatum, also known as St Johnís Wort, has received special attention due to
its pharmacological properties. Extracts from this plant are also utilized in
the treatment of mild to moderately severe depression. A novel protein, p27SJ
present in a laboratory callus culture of Hypericumperforatum suppresses transcription of
the HIV-1 genome in several human cell types including primary culture of microglia
and astrocytes. p27SJ associates with C/EBPβ,
a transcription factor that regulates expression of the HIV-1†† genome in macrophages and monocytic cells, and the viral transactivator,
Tat. It has been
found that it can suppress transcription of the HIV-1 genome. Despite its
importance, the three dimensional (3D) structure of p27SJ has not
yet been reported. A homology modeling method was used for
the prediction of the structure of p27SJ protein.For the modeling, template protein was obtained by Geno3D server, template protein pdb|2Q9T|chain A having identity 88%, E value 3e-129
and alignment Score 1140. By comparing the template protein a rough
model was constructed for the target protein using MODELLER, a program for
comparative modelling. The structure of p27SJ protein of Hypericumperforatum was found
to resemble the structure of peroxiredoxinhigh resolution structure of Ding Protein of Pseudomonas fluorescence. From Ramachandran plot analysis it
was found that the portion of residues falling into the most favoured regions
was 95.4%. The predicted 3-D model may be further characterized and analyzed using other techniques.